i'm a bit confused by your description.

the keys are associated with the original wow in the region.
if your cursor is on wow1... and you hit f8... which is tied to wow1/region1 ... then nothing will happen.
but, if you hit f9.. which it tied to wow2/region2... then wow1 and wow2 will swap.
at that point.. with your mouse hovering over wow2/region1 ... hitting f8 will bring wow1 back to region1.

basically... hitting the hotkey is always attached to the character you want.
(i hope that made sense)